The pioneer in cataloging Captured Japanese Maps is University of California, Berkeley. While not scanned at this writing, the library's bibliographic records for many of the map sets have served as a model for other institutions. Keyword search by the Romanized Japanese series title in their UCB Library Catalog.
Library of Congress may have one of the most extensive collection of Japanese imperial maps and charts in the world. It is not clear whether all their holdings have been cataloged. Japanese scholars have visited the library collection to photograph maps and charts to facilitate access back at their home institution in Japan. A few sheets of thousands have been scanned; a possible place to begin online viewing may be here. Cataloged records may be retrieved through an advanced search in their online catalog. The Geography and Map Division is creating a list of their holdings and interested researchers may contact Setsuko Means at smea [at] loc.gov.
Stanford University Libraries has scanned over 11,000 sheets of some 120 Gaihōzu map sets, making them available through their interactive index maps. There are different options for downloading. See their Gaihozu: Japanese Imperial Maps guide for more information.
Clark University has a finding aid to their holdings of some 10,000 sheets which can be found in their library catalog here.
The University of Connecticut has scanned their collection of Japanese military maps of Sakhalin here http://archives.lib.uconn.edu/islandora/object/20002%3ASakhalin?display=grid
There are many other American academic libraries holding Captured Japanese Maps--beneficiaries of an appreciative Army Map Service following World War II which established a program for distributing surplus military maps. (Hence, the AMS serial number stamped on sheets in the lower right corner.) From the initial 45 member depository libraries to 150, only 43 received captured Japanese and German maps according to a former Defense Mapping Agency staff member. (Nicoletti, Frank T. "US Army Topographic Command College Depository Program." Special Libraries Association Geography and Map Division Bulletin 86 (1971): 2-3.) Alternatively, details may be available from the National Archives which has a record box of the captured map distribution: NARA RG 226, Stack 190 5/30/7, Box #229.
The National Library of Australia has digitized their collection of most if not all of their Japanese imperial maps. The scanned maps are viewable in their TROVE digital repository. Search in Japanese or by the Romanized Japanese series title. Cataloged-only maps may be searched in the NLA online catalog.
For primary resources about Japanese imperial maps in our library here at Hamilton, there is the four-volume Gaihō sokuryō enkakushi (外邦測量沿革史).